small cleanup changes for CRAN submission

Author: JZauner

NEWS.md

@@ -1,5 +1,7 @@
 # LightLogR 0.5.3
 
+* small cleanup changes for CRAN submission
+
 # LightLogR 0.5.2
 
 * passed 300 unit tests for `LightLogR` 🎉

R/import_LL.R

@@ -194,7 +194,23 @@
 #'   
 #'   Model: GENEActiv
 #'   
-#'   **Note:** This import function takes GENEActiv data that was preprocessed through the [GGIR](https://cran.r-project.org/web/packages/GGIR/vignettes/GGIR.html) package. By default, `GGIR` aggregates light data into intervals of 15 minutes. This can be set by the `windowsizes` argument in GGIR, which is a three-value vector, where the second values is set to 900 seconds by default. To import the preprocessed data with `LightLogR`, the `filename` argument requires a path to the parent directory of the GGIR output folders, specifically the `meta` folder, which contains the light exposure data. Multiple `filename`s can be specified, each of which needs to be a path to a different GGIR parent directory. GGIR exports can contain data from multiple participants, these will always be imported fully by providing the parent directory. Use the `pattern` argument to extract sensible `Id`s from the *.RData* filenames within the *meta/basic/* folder. As per the author, [Dr. Vincent van Hees](https://accelting.com/), GGIR preprocessed data are always in local time, provided the `desiredtz`/`configtz` are properly set in GGIR. `LightLogR` still requires a timezone to be set, but will not timeshift the import data.
+#'   **Note:** This import function takes GENEActiv data that was preprocessed 
+#'   through the [GGIR]( https://cran.r-project.org/package=GGIR) package. 
+#'   By default, `GGIR` aggregates light data into intervals of 15 minutes. This
+#'   can be set by the `windowsizes` argument in GGIR, which is a three-value 
+#'   vector, where the second values is set to 900 seconds by default. To import
+#'   the preprocessed data with `LightLogR`, the `filename` argument requires a
+#'   path to the parent directory of the GGIR output folders, specifically the
+#'   `meta` folder, which contains the light exposure data. Multiple `filename`s
+#'   can be specified, each of which needs to be a path to a different GGIR 
+#'   parent directory. GGIR exports can contain data from multiple participants,
+#'   these will always be imported fully by providing the parent directory. Use
+#'   the `pattern` argument to extract sensible `Id`s from the *.RData* 
+#'   filenames within the *meta/basic/* folder. As per the author, 
+#'   [Dr. Vincent van Hees](https://www.accelting.com), GGIR preprocessed data are 
+#'   always in local time, provided the `desiredtz`/`configtz` are properly set
+#'   in GGIR. `LightLogR` still requires a timezone to be set, but will not
+#'   timeshift the import data.
 #'   
 #'   ## MotionWatch 8
 #'   

README.Rmd

@@ -47,7 +47,7 @@ To come:
 
 -   Integration of data into a unified database for cross-study analyses
 
-##### Please note that LightLogR is work in progress! If you are interested in the project and want to know more, you can subscribe to the [LightLogR mailing list](https://lists.lrz.de/mailman/listinfo/lightlogr-users). If you find a bug or would like to see new or improved features, please open an issue on the [GitHub repository](https://github.com/tscnlab/LightLogR/issues).
+##### Please note that LightLogR is work in progress! If you are interested in the project and want to know more, you can subscribe to the [LightLogR mailing list](https://www.tscnlab.org/software). If you find a bug or would like to see new or improved features, please open an issue on the [GitHub repository](https://github.com/tscnlab/LightLogR/issues).
 
 Have a look at the **Example** section down below to get started, or dive into the [Articles](https://tscnlab.github.io/LightLogR/articles/index.html) to get more in depth information about how to work with the package and generate images such as the one above, import data, visualization, and metric calculation.
 

README.md

@@ -59,7 +59,7 @@ To come:
 
 - Integration of data into a unified database for cross-study analyses
 
-##### Please note that LightLogR is work in progress! If you are interested in the project and want to know more, you can subscribe to the [LightLogR mailing list](https://lists.lrz.de/mailman/listinfo/lightlogr-users). If you find a bug or would like to see new or improved features, please open an issue on the [GitHub repository](https://github.com/tscnlab/LightLogR/issues).
+##### Please note that LightLogR is work in progress! If you are interested in the project and want to know more, you can subscribe to the [LightLogR mailing list](https://www.tscnlab.org/software). If you find a bug or would like to see new or improved features, please open an issue on the [GitHub repository](https://github.com/tscnlab/LightLogR/issues).
 
 Have a look at the **Example** section down below to get started, or
 dive into the

cran-comments.md

@@ -1,3 +1,32 @@
+## Submission Version 0.5.3
+
+### R CMD check results
+
+0 errors ✔ | 0 warnings ✔ | 3 notes ✖
+
+* Note 1: Imports includes 22 non-default packages. 
+  This is correct and necessary
+
+* Note 2: unable to verify current time. 
+  Time server seems to be unavailable
+
+* Note 3: Found HTML validation problems. 
+  This note seems related to the testing environment and not the actual package.
+
+### Windevel results
+
+2 Notes
+
+* Note: Author field differs from that derived from Authors@R.
+  As far as I can tell, the only difference is that the Authors@R field has (ORCID: *Orcid URL*) behind the authors, where as the Author field has (*Orcid URL*). As this is automatically generated based on Description, I don't think I can influence that.
+
+* Note: Examples with CPU (user + system) or elapsed time > 10s
+                user system elapsed
+  gg_photoperiod 12.52   1.72   14.25
+  gg_doubleplot   9.45   1.39   10.85
+
+  These examples are expected to take a longer time, as they are plotting functions and several variants are shown in the examples.
+
 ## Resubmission #3 (Version 0.3.8)
 
 This is a resubmission. In this version I corrected the error in a symlog_trans example.